January 20, 2012

It seems that Michael Hammer was good on his promise that in 2012 "This year, we should be able to confirm what we found and go way beyond that." In a new paper, conclusive evidence is presented about introgression of an archaic sequence into Melanesian populations. The argument is as follows:

Melanesians are more diverse in that region than Africans.

The common ancestor of the "archaic" and "African" haplotypes lived >3 million years ago.

The "archaic" haplotype matches the ancient DNA from the Denisova hominin.

Balancing selection (which can sometimes maintain extremely old polymorphism) is not reasonable in this case, because it would need to maintain both "archaic" and "African" haplotypes for a long time, but then (inexplicably) would continue to operate in Melanesia and cease to operate everywhere else.

Notice that once again, this is based on resequencing a small region of the genome. This is why I am all the more confident in my prediction that the advent of full genome sequencing will uncover more archaic admixture in humans. It may not always be able to use all the above listed criteria to confirm this admixture (since we do not and cannot have ancient DNA from all the archaic hominins that once roamed the planet), but all the remaining ones will suffice to make a very good case for introgression.

What I find particularly interesting, is that Mendez et al. re-iterate a few times that genomewide averages admit to different explanations:

Full genome comparisons of the Neandertal and Denisova draft genomes with modern human sequences have revealed different amounts of shared ancestry between each of these archaic forms and anatomically modern human (AMH) populations from different geographic regions. For example, a higher proportion of SNPs was shared between non-African and Neandertal, and between Melanesian and the Denisova genomes, than between either Neandertal or Denisova and extant African genomes (Green et al. 2010; Reich et al. 2010). An intriguing possibility is that these patterns result from introgression of archaic genes into AMH populations in Eurasia. However, this SNP sharing pattern could also be explained by ancestral population structure in Africa (i.e., without the need to posit introgression). For example, if non-Africans and the ancestors of Neandertals descend from the same deme in a subdivided African population, and this structure persisted with low levels of gene flow among African residents until the ancestors of non-Africans migrated into Eurasia, then we would expect more SNP sharing between non-Africans and Neandertals (Durand et al. 2011).

...

While genome-wide comparisons detect more sequence agreement between non-African and Neandertal genomes, and between Melanesian and Denisova genomes, the specific loci exhibiting these signals have not yet been identified. Furthermore, current analyses do not elucidate the relative roles of recent introgression versus long-term population structure in Africa in explaining these patterns.

The current paper does a good job at showing how in one particular region archaic introgression into Melanesians is indeed the best explanation for the evidence. But, the fact that the authors seem to re-iterate the possibility of African population structure and repeatedly caution against using patterns of genomewide sharing between modern and archaic humans is a strong hint that there are more things to come on the topic.

We should remember that the widely-circulated estimates of Neandertal->Eurasian introgression are based on genomewide averages. It is true that Reich et al. (2010) identified 13 regions of potential Neandertal introgression, which together make up a very small portion of the human genome. So, the jury is out on whether African population structure or Neandertal introgression is responsible for most of the genomewide pattern.

What you can be sure of is that many scientists are busy lining up full genomes from different human populations as we speak, and finding plenty of regions where haplotypes of extremely old divergence times co-exist in our species. We will probably learn more about such efforts during 2012.

Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1 gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

12 comments:

There is also the recently highlighted issue that the Vindija Neanderthals used in the preparation of the Neanderthal draft genome might have significant modern human admixture. So there is enough reason to regard the current Neanderthal-to-modern human gene flow percentages with suspicion.

In most cases of successful mammalian hybridization, which female animal is most likely to produce (give birth to) offspring which is both ~viable and reasonably ~fertile: the superior of the two species bred, or the inferior of the two?

Answer: the superior of the two species bred. A female of the inferior species mated, will usually miscarry; or if it should miraculously give live birth somehow, the offspring will almost undoubtedly be sterile (ie unable to reproduce).

Which is most ~primitive taxonomically: the mare horse from which a mule is foaled, or the mule foal?

(I would assume the donkey sire to be the most taxonomically primitive of the three parties involved in procreating a hybrid mule).

The only way to evolve a horse from a mule, would be to backbreed mules with only purebred horses, for many generations -- but regardless, the offspring would still retain some fraction of their male donkey ancestor's DNA in them.

However, their mtDNA would always be that of a horse; because it would be irrational (ie largely biologically unsuccessful, and contrary to the working, practical theory of mammalian hybridization) to breed a mule mare with a stud horse.

"Answer: the superior of the two species bred. A female of the inferior species mated, will usually miscarry; or if it should miraculously give live birth somehow, the offspring will almost undoubtedly be sterile"

Surely it depends on what you consider to be the 'superior of the two species'. I don't follow your logic tha horses are 'superior' to donkeys. They are simply two different species.

"I would assume the donkey sire to be the most taxonomically primitive of the three parties involved in procreating a hybrid mule"

Three parties? Surely just two: horse and donkey. The cross either way gives viable, but usually sterile, offspring. The haorse is usually used as the female side because it produces a larger foal. But it is the offspring of a male horse and a female donkey (a 'hinny') that is more often fertile than is the cross the other way. Sort of destroys your argument.

"Surely it depends on what you consider to be the 'superior of the two species'..."

It's a question of context: a practical matter, not one of aesthetics: ie mares & jacks are chosen for breeding mules, b/c otherwise (due to chromosomal differences between sp. E. asinus and sp. E. caballus) you'd have a hybrid hinny, instead of a hybrid mule - not that we hate or look down on donkeys.

The colloquialism, "superior", is commonly used by breeders or agriculturalists when comparing two species being considered for hybridization. It refers to the more biologically complex of the two compared, having nothing to do with politics.

I admit that for the sake of context, a better word used here might havebeen "dominant". "Superior" implies being above or over ~physically or ~spatially (see medical and biological definitions); whereas "dominant" (somewhat more abstractly) implies being above or over, ~taxonomically, in classification.

"Three parties? Surely just two: horse and donkey. The cross either way gives viable, but usually sterile, offspring. The haorse is usually used as the female side because it produces a larger foal. But it is the offspring of a male horse and a female donkey (a 'hinny') that is more often fertile than is the cross the other way. Sort of destroys your argument."

--Horses and donkeys are different species, with different numbers of chromosomes. Of the two F1 hybrids between these two species, a mule is easier to obtain than a hinny (the offspring of a male horse and a female donkey). All male mules and most female mules are infertile.--http://en.wikipedia.org/wiki/Mule

--Since 1527 there have been more than sixty documented cases of foals born to female mules around the world. In contrast, according to the ADMS, there is only one known case of a female hinny doing so.--http://en.wikipedia.org/wiki/Hinny#Fertility.2C_sterility.2C_and_rarity

Commonplace mules, easier to produce from mares+jacks than rare hinnys from jennets+stallions, always possess & produce offspring w/ the mtDNA of mares (ie horses, the 'dominant' of the two parent species).

Hinnys always have the mtDNA of jennets (female donkeys), but are virtually 100% sterile, both male & female; so don't reproduce at all compared to mules, which when bred w/ horses or donkeys do reproduce (although at lower rates of fecundity than either horses or donkeys).

That's why I consider the offspring 'party' to transactions of mammalian inter-species hybridization.

"No. But it is more likely that the donkey is a more recent evolutionary product that is a horse. They and zebras moved further from America than did the horse."

The question was, which came first, hybrid mules or pure species horses?

Interesting point however, about horses originating in the Americas. Without regard to intentional selective breeding by Human captors, why do you suppose wild horses became extinct there, along with mammoths & certain other large mammals (tigers, etc.) similar to ones still in existence today - yet in different forms - in the Eastern Hemisphere? I assume it had something to do with climate changes.

However, due to the differing numbers of chromosomes, & the fact that horses & donkeys co-exist as separate species, I don't see how the donkey could have evolved from horses.http://www.bucknell.edu/msw3/browse.asp?id=14100002

"There is no reason at all why Neanderthals and 'Denisovans'could not have left genes in the modern human population."

They did obviously leave their genes w/ us, just as mares & jacks leave their genetic imprint on hybrid mule offspring; that was my point. And as with other hybrids or pure species mammals, we only inherit the mtDNA of our ~mothers.

That is why all ancient remains of Neanderthals tested, have had Human mitochondria (the 'dominant' of the two species bred to create them, according to the principles of Mammalian Hybrid Theory).

And I expect they have only ~particular clades of ancient Human mtDNA, (since the event(s) which bred them through inter-species hybridization, occured many ages ago).

If you BLAST your DNA against Neanderthals' mtDNA alone, you get the same results as when comparing against standard Human mtDNA: ~99% identities.

It's only when comparing the whole genomes of 'anatomically modern' Humans with that of Neanderthals, that we may see significant variances among the Human population: some people more closely match the Neanderthal hybrid's DNA than do others.

I expect those people who match, have deep ancestry in the same regions where the Neanderthal arose and dispersed. And in fact, they do so.

Yet there are other ancient hybrid types, such as the Denisovan, which have also left their genetic evidence in modern humans. We ought to be able to figure out which hybrids (if any) we are descended from - based on our DNA... perhaps even based simply on our blood chemistry.

Hybridization triggers genetic mutations, resulting in the astonishing arrays of different types of mtDNA and yDNA (& the other kinds: chromosomal, autosomal, etc., along with blood groups & types) present in the modern 'Human species'.

There is more quantitative genetic ~distance between male & female humans, OR between some human races or ethnic groups -- than is found between the entire Human species as a whole, when compared to Chimpanzees!

Because there were at some point(s) in ancient history, ~events or ~incidents of inter-species hybridization involving Human beings (Homo Sapiens sapiens). And I'm afraid it wasn't that they mated with 'fallen angels' or 'ET's.

In order to understand the true origin(s) of Human beings (including the many 'anatomically modern' varieties), you must familiarize yourself w/ the ~biological definitions of the terms "evolution" and "descent". It's important to know that they have different meanings in anthropology. Many people also confuse "descent" with "evolution", using the two terms interchangibly.

evolution[L. e-, out + volvere, to roll]All the changes that have transformed life on Earth from its earliest beginnings to the diversity that characterizes it today.

Understanding the origins of Humanity involves multiple disciplines of study. It's yet another area where "specialization" is not necessarily a 'good thing'.

All of my elaborate "horse talk" is for the purpose of an easily understandable ~example. The same basic principles of hybrid theory apply to virtually any two mammalian species close enough taxonomically to breed. It applies to hybrid hominids as well.http://en.wikipedia.org/wiki/Hominidae

That's like saying humans evolved from chimpanzees. In both cases both species evolved from a common ancestor.

"why do you suppose wild horses became extinct there, along with mammoths & certain other large mammals (tigers, etc.) similar to ones still in existence today - yet in different forms - in the Eastern Hemisphere? I assume it had something to do with climate changes".

More likely human hunting, or human alteration of the lanscape by elimination of the megafauna.

"I expect those people who match, have deep ancestry in the same regions where the Neanderthal arose and dispersed".

I agree completely with that.

"Because there were at some point(s) in ancient history, ~events or ~incidents of inter-species hybridization involving Human beings (Homo Sapiens sapiens)".

And I agree with that. Such hybridization almost certainly goes back to before the origin of Australopithecus and has continued since.

"That is why all ancient remains of Neanderthals tested, have had Human mitochondria"

That is incorrect. Most Neanderthal mtDNA does not belong to any known modern human haplogroups.

"If you BLAST your DNA against Neanderthals' mtDNA alone, you get the same results as when comparing against standard Human mtDNA: ~99% identities".

But you never 'blast' mtDNAs together. MtDNA is passed only from mother to daughter, usually completely unchanged.

"Commonplace mules, easier to produce from mares+jacks than rare hinnys from jennets+stallions, always possess & produce offspring w/ the mtDNA of mares (ie horses, the 'dominant' of the two parent species)".

No. Mules have horse mtDNA because the mtDNA always comes from the mother. That's why 'Hinnys always have the mtDNA of jennets (female donkeys)'.

"Hybridization triggers genetic mutations"

Not so. Hybridization triggers new mixtures of genes from the two contributing populations, and sometimes these can have unforseen effects.

"the astonishing arrays of different types of mtDNA and yDNA"

Hybridization doesn't 'change' either. In fact it is sometimes possible to work out the contributing populations because the male and female lines come from different populations. That fact makes the Polynesians particularly revealing.

"The question was, which came first, hybrid mules or pure species horses?"

The answer is obvious. It is impossible to have a 'hybrid mule' until you have 'pure species horses'.

"It's a question of context: a practical matter, not one of aesthetics: ie mares & jacks are chosen for breeding mules, b/c otherwise (due to chromosomal differences between sp. E. asinus and sp. E. caballus) you'd have a hybrid hinny, instead of a hybrid mule"

The chromosome difference applies whichever direction the hybrid occurrs. The reason 'mares & jacks are chosen for breeding mules' is because mares produce larger offspring than do donkeys, and mules are used for work so size matters. That's why hinnys are so rare. They're useless for anything.

"--Horses and donkeys are different species, with different numbers of chromosomes".

Chromosome difference is not necessarily a probalem because Przewalski's horses and domestic horses have different chromosome numbers yet produce fertile offspring. In fact that has become a problem for maintaining the purity of Przewalski's horses.

"The colloquialism, 'superior', is commonly used by breeders or agriculturalists when comparing two species being considered for hybridization. It refers to the more biologically complex of the two compared"

I have had a great deal to do with agriculture and animal and plant hybridization, and I have never heard such a reference. Hybrids are utilized to obtain the most useful characteristics of each breed.

"All of my elaborate 'horse talk' is for the purpose of an easily understandable ~example. The same basic principles of hybrid theory apply to virtually any two mammalian species close enough taxonomically to breed".

"I have had a great deal to do with agriculture and animal and plant hybridization, and I have never heard such a reference. Hybrids are utilized to obtain the most useful characteristics of each breed."

Definition of 'Species' from Saunders Veterinary Dictionary: "A taxonomic category subordinate to a genus (or subgenus) and SUPERIOR to a subspecies or variety..."

The term "superior" used in the same context as in my OP (ie regarding zoological or biological ~taxonomy).

"What about hybrid vigour?"

http://www.demogr.mpg.de/longevityrecords/0203.htmHumans already enjoy the longest lifespans of any mammal. How would inter-species crossing improve that?

And I certainly don't believe it's worth the trade-off in IQ points, just for a random chance of possible increased 'vigor'.

(Most lethal diseases in Humans - ones against which we have no 'immunity' - ~originate via contact w/ foreign animal species or unfamiliar Human populations.)

In my OP, I was talking about ~inter-species hybridization with Humans (ie Human x Rhesus macaque or Human x Chimpanzee) not about simple outbreeding between different races of the same species.

Donkeys & horses aren't different races of the same species - they're distinctly different species, w/ different numbers of chromosomes).

You breed Humans w/ lower apes, & you ~might get some "hybrid vigor" out of it - but you surely will also get a substantial loss of ~IQ in the offspring.

(Evidently, Neanderthals were the hybrid offspring of Humans x Rhesus monkeys; which then were subsequently ~backbred into the Human population.)

Many gardeners prefer heirloom varieties of seeds over hybrids, for very good reasons (better flavor, better results from propagation of saved seeds (most people don't bother saving the seeds of hybrid crops, due to the unpredictable nature of their growth and development).http://urbanext.illinois.edu/hortihints/0102a.html

Hybrid vigor is great for breeding fruit flies in labs or for corporate profits, ie ConAgra; but there's a trade-off in every instance of either inter-species or intra-species crossing.

The biggest trade-off in intra-species hybridization, is the sacrifice of the natural, healthy balance of eco-systems.

(Btw, the term "superior" or "superiority" is often used in rhetoric about hybridization's supposed advantages.)

"Definition of 'Species' from Saunders Veterinary Dictionary: 'A taxonomic category subordinate to a genus (or subgenus) and SUPERIOR to a subspecies or variety...'"

They mean 'superior' only in terms of nomenclature. Nothing to do with any genetic superiority. In othwer words nomenclature goes: genus, species, subspecies, with 'genus' being superior to 'species'. The idea certainly cannot be applied to the use of two species during the formation of a hybrid. Anyway, in agricutlural circles what on earth would be the reason for crossing any two species if one was genetically inferior?

"Humans already enjoy the longest lifespans of any mammal. How would inter-species crossing improve that?'

It's very doubtful that any humans could form hybrids with any living species. However it by no means follows that they were necessarily unable to form fertile hybrids with species now extinct. Hybrid vigour is not usually a product of between species hybrids. It occurrs within separate populations of the same species.

"And I certainly don't believe it's worth the trade-off in IQ points, just for a random chance of possible increased 'vigor'"

Exactly why farmers would not cross two species if both were not economically useful. It is the combination of useful characteristics they are after.

"In my OP, I was talking about ~inter-species hybridization with Humans (ie Human x Rhesus macaque or Human x Chimpanzee) not about simple outbreeding between different races of the same species".

Even chimpanzees are too remote from humans genetically to form hybrids. In general the time since separation for two species to be capable of forming hybrids is something in the order of a million years. Of course it's not specifically time dependent.

"Donkeys & horses aren't different races of the same species - they're distinctly different species, w/ different numbers of chromosomes)"

I keep trying to tell you that chromosome number is irrelevant. Obviously horses and donkeys have not been separated long enough to be unable to form hybrids.

"You breed Humans w/ lower apes, & you ~might get some 'hybrid vigor' out of it"

Extremely unlikely to be able to do it in the first place.

"Evidently, Neanderthals were the hybrid offspring of Humans x Rhesus monkeys; which then were subsequently ~backbred into the Human population"

Where on earth did you get that information from?

"Many gardeners prefer heirloom varieties of seeds over hybrids, for very good reasons (better flavor, better results from propagation of saved seeds"

Very true. But hybrids are used commercially because the production is greater with careful selection of the parent and grandparent species. For example hybrid hens lay far more eggs than do any 'heirloom varieties' of poultry.

"most people don't bother saving the seeds of hybrid crops, due to the unpredictable nature of their growth and development"

But that is the point of using hybrids. Their ancestry is selected to bring out the best points of each in the final cross. The F2 generation can throw up any combination of characteristics of the ancestral varieties.

terryt - "...what on earth would be the reason for crossing any two species if one was genetically inferior?"

terryt - "... doubtful... it by no means follows that they were necessarily unable to form fertile hybrids with species now extinct."

terryt - "... economically useful..."

terryt - "Even chimpanzees are too remote from humans genetically to form hybrids."

terryt - "Where on earth did you get that information from?"

~~ Despite all their rhetoric about enhancing the performance of bodily functions, the posthuman project is nevertheless driven by a hatred and loathing of the body. Extending longevity and improving physical and mental functions is merely an interim strategy until such time that virtual immortality is achieved, liberating humans from their weak and fragile bodies. Yet is not this high-tech Manichean dream tantamount, as Paul Ramsey once observed, to a suicidal death-wish for the human species? ~~ Dr. Calum Mackellar, the Center for Bioethics and Human Dignity

~~ ... geneticist David Reich of the Broad Institute at Harvard and M.I.T. has advanced a theory that the bishop’s wife would have found even more disturbing: human and chimp ancestors, after diverging into separate species millions of years ago, came back together and interbred.

~~ Reich came up with the idea after comparing the genes of humans and chimps. When two species split from a common ancestor, their genes will continue to diverge, or mutate, at a regular clip over time. Reich and his team of researchers, after comparing some 20 million base pairs (the “rungs” of DNA) from humans and chimps, found that different genes began diverging at different times — with genes located on the X chromosome of humans and chimps parting ways most recently.

~~ Reich’s explanation is that the two populations interbred on repeated occasions over hundreds of thousands, if not millions, of years, producing hybrids of protohumans and protochimps. The male hybrids were likely to be sterile, but Reich posits that the female hybrids (with their two X chromosomes) were able to mate with males of one of the original species. This would explain why genes on the X chromosome of humans and chimps diverged more recently. ~~

[Which begs the question: If Humans were going to subsequently breed themselves back into some of earth's native lower primate populations (some of which may be extinct now) following speciation - why have naturally divergent species in the first place? It seems that Mankind has just enough intelligence to get itself into deep trouble.]

terryt - "Extremely unlikely to be able to do it in the first place."

~~ ...YTT [Toba supervolcano eruption in Indonesia] may have forced our ancestors to adopt new survival strategies, which permitted them to replace Neanderthals and "other archaic human species". However, both Neanderthals in Europe and the small-brained Homo floresiensis in Southeastern Asia survived YTT by 50,000 and 60,000 years respectively... ~~

http://en.wikipedia.org/wiki/Toba_catastrophe_theory

[It's altogether probable, that Human beings in fact ~created (ie ~bred, as when breeding mules) the "archaic hominid" (note that this term was in quotations in the Wikipedia article, too, because it hasn't been proven that Neanderthal, Denisovan, etc., are older species than Humans; in fact the genetic evidence points to them being Human ~sub-species) which are proven Hybrids.]

"geneticist David Reich of the Broad Institute at Harvard and M.I.T. has advanced a theory that the bishop’s wife would have found even more disturbing: human and chimp ancestors, after diverging into separate species millions of years ago, came back together and interbred".

Here's the paper:

http://genepath.med.harvard.edu/~reich/Patterson%20et%20al.2.pdf

What aspect of it is so surprising to you? As the two species diverged there would have been no magical moment in time when they were suddenly unable to form hybrids. The drift apart would basically have been gradual.

"Which begs the question: If Humans were going to subsequently breed themselves back into some of earth's native lower primate populations (some of which may be extinct now) following speciation - why have naturally divergent species in the first place?"

What do you mean by, 'why have naturally divergent species'? Sounds as though you believe evolution moves in a particular direction, controlled by some supernatural power? Speciation simply occurrs as populations split an develop in their own direction. If they happen to meet again before speciation is complete they are quite capable of interbreeding still. And on what grounds can you really claim to know that over the period of hybridization the line that was to give rise to humans was somehow 'superior' to the other line?

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